{"id":"https://openalex.org/W2611390736","doi":"https://doi.org/10.1093/bioinformatics/btx282","title":"Exploring spatially adjacent TFBS-clustered regions with Hi-C data","display_name":"Exploring spatially adjacent TFBS-clustered regions with Hi-C data","publication_year":2017,"publication_date":"2017-05-03","ids":{"openalex":"https://openalex.org/W2611390736","doi":"https://doi.org/10.1093/bioinformatics/btx282","mag":"2611390736","pmid":"https://pubmed.ncbi.nlm.nih.gov/28472433"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btx282","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx282","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/17/2611/25163889/btx282.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/33/17/2611/25163889/btx282.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5057117181","display_name":"Hebing Chen","orcid":"https://orcid.org/0000-0003-4102-356X"},"institutions":[{"id":"https://openalex.org/I4210132047","display_name":"Beijing Radiation Center","ror":"https://ror.org/030t7nd77","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210132047"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hebing Chen","raw_affiliation_strings":["Beijing Institute of Radiation Medicine, Beijing, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Beijing Institute of Radiation Medicine, Beijing, China","institution_ids":["https://openalex.org/I4210132047"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041686947","display_name":"Shuai Jiang","orcid":"https://orcid.org/0000-0002-9737-9744"},"institutions":[{"id":"https://openalex.org/I4210132047","display_name":"Beijing Radiation Center","ror":"https://ror.org/030t7nd77","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210132047"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shuai Jiang","raw_affiliation_strings":["Beijing Institute of Radiation Medicine, Beijing, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Beijing Institute of Radiation Medicine, Beijing, China","institution_ids":["https://openalex.org/I4210132047"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100429706","display_name":"Zhuo Zhang","orcid":"https://orcid.org/0000-0002-2944-1526"},"institutions":[{"id":"https://openalex.org/I4210132047","display_name":"Beijing Radiation Center","ror":"https://ror.org/030t7nd77","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210132047"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhuo Zhang","raw_affiliation_strings":["Beijing Institute of Radiation Medicine, Beijing, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Beijing Institute of Radiation Medicine, Beijing, China","institution_ids":["https://openalex.org/I4210132047"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100348617","display_name":"Hao Li","orcid":"https://orcid.org/0000-0002-6294-6761"},"institutions":[{"id":"https://openalex.org/I4210132047","display_name":"Beijing Radiation Center","ror":"https://ror.org/030t7nd77","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210132047"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hao Li","raw_affiliation_strings":["Beijing Institute of Radiation Medicine, Beijing, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Beijing Institute of Radiation Medicine, Beijing, China","institution_ids":["https://openalex.org/I4210132047"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020533472","display_name":"Yiming Lu","orcid":"https://orcid.org/0000-0001-8005-2705"},"institutions":[{"id":"https://openalex.org/I4210132047","display_name":"Beijing Radiation Center","ror":"https://ror.org/030t7nd77","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210132047"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Yiming Lu","raw_affiliation_strings":["Beijing Institute of Radiation Medicine, Beijing, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Beijing Institute of Radiation Medicine, Beijing, China","institution_ids":["https://openalex.org/I4210132047"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5045958734","display_name":"Xiaochen Bo","orcid":"https://orcid.org/0000-0003-1911-7922"},"institutions":[{"id":"https://openalex.org/I4210132047","display_name":"Beijing Radiation Center","ror":"https://ror.org/030t7nd77","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210132047"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Xiaochen Bo","raw_affiliation_strings":["Beijing Institute of Radiation Medicine, Beijing, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Beijing Institute of Radiation Medicine, Beijing, China","institution_ids":["https://openalex.org/I4210132047"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5020533472","https://openalex.org/A5045958734"],"corresponding_institution_ids":["https://openalex.org/I4210132047"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.03836703,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"33","issue":"17","first_page":"2611","last_page":"2614"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9911999702453613,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9911999702453613,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10268","display_name":"Developmental Biology and Gene Regulation","score":0.004600000102072954,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.0012000000569969416,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.43784862756729126},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.32682302594184875},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.28838998079299927}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.43784862756729126},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.32682302594184875},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.28838998079299927}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002460","descriptor_name":"Cell Line","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002460","descriptor_name":"Cell Line","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002460","descriptor_name":"Cell Line","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D053595","descriptor_name":"Embryonic Stem Cells","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D053595","descriptor_name":"Embryonic Stem Cells","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D053595","descriptor_name":"Embryonic Stem Cells","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btx282","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx282","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/17/2611/25163889/btx282.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:28472433","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28472433","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:5860062","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5860062","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btx282","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx282","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/17/2611/25163889/btx282.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4111034471","display_name":null,"funder_award_id":"U1435222","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":13,"referenced_works":["https://openalex.org/W1994536648","https://openalex.org/W2011463791","https://openalex.org/W2014677321","https://openalex.org/W2029426610","https://openalex.org/W2065006553","https://openalex.org/W2070021921","https://openalex.org/W2078455244","https://openalex.org/W2084191969","https://openalex.org/W2090037139","https://openalex.org/W2107575419","https://openalex.org/W2135185213","https://openalex.org/W2148966035","https://openalex.org/W2462894283"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2382290278","https://openalex.org/W2478288626","https://openalex.org/W2350741829","https://openalex.org/W2530322880","https://openalex.org/W1596801655"],"abstract_inverted_index":{"MOTIVATION:":[0],"Transcription":[1],"factor":[2],"binding":[3],"sites":[4],"(TFBSs)":[5],"are":[6,47,151],"clustered":[7],"in":[8,43,66],"the":[9,13,112,118,122,126,134,139],"human":[10,128],"genome,":[11],"forming":[12,61],"TFBS-clustered":[14,40,45,59,72,88,114],"regions":[15,41,46,60,89,115],"that":[16,85,100],"regulate":[17,95],"gene":[18,67],"transcription,":[19],"which":[20,44],"requires":[21],"dynamic":[22],"chromatin":[23],"configurations":[24],"between":[25,111],"promoters":[26,68],"and":[27,137],"distal":[28,87],"regulatory":[29,35,141],"elements.":[30],"Here,":[31],"we":[32],"propose":[33],"a":[34,77,101],"model":[36],"called":[37],"spatially":[38],"adjacent":[39],"(SATs),":[42],"connected":[48],"by":[49,54,107],"spatial":[50],"proximity":[51],"as":[52,76],"identified":[53],"high-resolution":[55],"Hi-C":[56],"data.":[57],"RESULTS:":[58],"SATs":[62,75,93,108],"appeared":[63,79],"less":[64],"frequently":[65],"than":[69],"did":[70],"isolated":[71],"regions,":[73],"whereas":[74],"whole":[78],"more":[80],"frequently.":[81],"These":[82],"observations":[83],"indicate":[84],"multiple":[86],"combined":[90],"to":[91,94],"form":[92],"genes.":[96],"Further":[97],"examination":[98],"confirmed":[99],"substantial":[102],"portion":[103],"of":[104,117,125],"genes":[105],"regulated":[106],"were":[109],"located":[110],"paired":[113],"instead":[116],"downstream.":[119],"We":[120],"reconstructed":[121],"chromosomal":[123],"conformation":[124],"H1":[127],"embryonic":[129],"stem":[130],"cell":[131],"line":[132],"using":[133],"ShRec3D":[135],"algorithm":[136],"proposed":[138],"SAT":[140],"model.":[142],"CONTACT:":[143],"ylu.phd@gmail.com":[144],"or":[145],"boxc@bmi.ac.cn.":[146],"SUPPLEMENTARY":[147],"INFORMATION:":[148],"Supplementary":[149],"data":[150],"available":[152],"at":[153],"Bioinformatics":[154],"online.":[155]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
